The kidney matrisome in health, aging, and disease
Authors: Franziska Lausecker, Rachel Lennon, Michael J. Randles
Journal: Kidney International (2022)

Dysregulated extracellular matrix is the hallmark of fibrosis, and it has a profound impact on kidney function in disease. Furthermore, perturbation of matrix homeostasis is a feature of aging and is associated with declining kidney function. Understanding these dynamic processes, in the hope of developing therapies to combat matrix dysregulation, requires the integration of data acquired by both well-established and novel technologies. Owing to its complexity, the extracellular proteome, or matrisome, still holds many secrets and has great potential for the identification of clinical biomarkers and drug targets. The molecular resolution of matrix composition during aging and disease has been illuminated by cutting-edge mass spectrometry–based proteomics in recent years, but there remain key questions about the mechanisms that drive altered matrix composition. Basement membrane components are particularly important in the context of kidney function; and data from proteomic studies suggest that switches between basement membrane and interstitial matrix proteins are likely to contribute to organ dysfunction during aging and disease. Understanding the impact of such changes on physical properties of the matrix, and the subsequent cellular response to altered stiffness and viscoelasticity, is of critical importance. Likewise, the comparison of proteomic data sets from multiple organs is required to identify common matrix biomarkers and shared pathways for therapeutic intervention. Coupled with single-cell transcriptomics, there is the potential to identify the cellular origin of matrix changes, which could enable cell-targeted therapy. This review provides a contemporary perspective of the complex kidney matrisome and draws comparison to altered matrix in heart and liver disease. Dysregulated extracellular matrix is the hallmark of fibrosis, and it has a profound impact on kidney function in disease. Furthermore, perturbation of matrix homeostasis is a feature of aging and is associated with declining kidney function. Understanding these dynamic processes, in the hope of developing therapies to combat matrix dysregulation, requires the integration of data acquired by both well-established and novel technologies. Owing to its complexity, the extracellular proteome, or matrisome, still holds many secrets and has great potential for the identification of clinical biomarkers and drug targets. The molecular resolution of matrix composition during aging and disease has been illuminated by cutting-edge mass spectrometry–based proteomics in recent years, but there remain key questions about the mechanisms that drive altered matrix composition. Basement membrane components are particularly important in the context of kidney function; and data from proteomic studies suggest that switches between basement membrane and interstitial matrix proteins are likely to contribute to organ dysfunction during aging and disease. Understanding the impact of such changes on physical properties of the matrix, and the subsequent cellular response to altered stiffness and viscoelasticity, is of critical importance. Likewise, the comparison of proteomic data sets from multiple organs is required to identify common matrix biomarkers and shared pathways for therapeutic intervention. Coupled with single-cell transcriptomics, there is the potential to identify the cellular origin of matrix changes, which could enable cell-targeted therapy. This review provides a contemporary perspective of the complex kidney matrisome and draws comparison to altered matrix in heart and liver disease. Extracellular matrix plays a critical role in normal tissue architecture, and matrix dysregulation leads to fibrosis, which contributes to 45% of deaths worldwide.1Wynn T.A. Cellular and molecular mechanisms of fibrosis.J Pathol. 2008; 214: 199-210Crossref PubMed Scopus (2956) Google Scholar Fibrosis is an excessive accumulation of matrix and is a common injury response observed across numerous kidney diseases.2Hewitson T.D. Fibrosis in the kidney: is a problem shared a problem halved?.Fibrogenesis Tissue Repair. 2012; 5: S14Crossref PubMed Scopus (55) Google Scholar As fibrosis is detected histologically, it serves as a diagnostic tool for progressive kidney disease.3Farris A.B. Alpers C.E. 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Giacchetti G. et al.Multiple regulatory inputs converge on cortactin to control invadopodia biogenesis and extracellular matrix degradation.J Cell Sci. 2008; 121: 369-378Crossref PubMed Scopus (169) Google Scholar This synergistic relationship means that perturbation of matrix has profound implications for tissue composition and function. To understand matrix dysregulation in disease, it is a prerequisite to define the matrix in health. In 2009, a novel matrix database, MatrixDB, was introduced, recording the interactions between known matrix components. The first iteration in 2009 contained 259 extracellular biomolecules and 1972 interactions,22Chautard E. Ballut L. Thierry-Mieg N. MatrixDB Ricard-Blum S. a database focused on extracellular protein-protein and protein-carbohydrate interactions.Bioinformatics. 2009; 25: 690-691Crossref PubMed Scopus (0) Google Scholar whereas the latest version of MatrixDB contains 106,543 matrix interactions.23Berthollier C. Vallet S.D. 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The extracellular matrix at a glance.J Cell Sci. 2010; 123: 4195-4200Crossref PubMed Scopus (2193) Google Scholar The relative abundance and cross-linking of these components define tissue properties (e.g., stiffness).26Martinez-Vidal L. Murdica V. Venegoni C. et al.Causal contributors to tissue stiffness and clinical relevance in urology.Commun Biol. 2021; 4: 1011Crossref PubMed Scopus (5) Google Scholar Matrix organizes into 2 distinct entities with different functions. Whilst interstitial matrices give tissues structural support, sheet-like basement membranes underlie continuous layers of cells, including muscle, nerve, endothelial, and epithelial cells. Whereas interstitial matrices mainly comprise fibrillar collagens, basement membranes contain laminins and network-forming type IV collagen (Figure 1). Beyond these 2 core networks, basement membranes are highly complex macromolecular structures, and >200 components have been localized to different basement membranes.27Jayadev R. 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This review outlines our current understanding of the kidney matrisome in the context of health, aging, and disease and draws comparisons to altered matrix in other organs. Transcriptomics has been used, with great effect, to study the molecular changes in kidney disease in an unbiased manner.35Hodgin J.B. Borczuk A.C. Nasr S.H. et al.A molecular profile of focal segmental glomerulosclerosis from formalin-fixed, paraffin-embedded tissue.Am J Pathol. 2010; 177: 1674-1686Abstract Full Text Full Text PDF PubMed Scopus (0) Google Scholar, 36Ju W. Greene C.S. Eichinger F. et al.Defining cell-type specificity at the transcriptional level in human disease.Genome Res. 2013; 23: 1862-1873Crossref PubMed Scopus (145) Google Scholar, 37Reich H.N. Tritchler D. Cattran D.C. et al.A molecular signature of proteinuria in glomerulonephritis.PLoS One. 2010; 5e13451Crossref PubMed Scopus (51) Google Scholar, 38Berthier C.C. Bethunaickan R. 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Pickard A. et al.Circadian control of the secretory pathway maintains collagen homeostasis.Nat Cell Biol. 2020; 22: 74-86Crossref PubMed Scopus (74) Google Scholar The matrix was an understudied proteome but has benefitted from advances in technology in the past 10 years. The prior limited progress in matrix research was due to a combined perception of its role as an inert scaffold, compounded by seemingly unsurmountable technical challenges.44Byron A. Humphries J.D. Humphries M.J. Defining the extracellular matrix using proteomics.Int J Exp Pathol. 2013; 94: 75-92Crossref PubMed Scopus (106) Google Scholar Matrix is highly cross-linked and insoluble, limiting most standard biochemical analysis protocols. However, the progression of proteomic technologies combined with the advent of refined protocols has heralded a new era of matrix research. Matrix enrichment approaches24Naba A. Clauser K.R. Hoersch S. et al.The matrisome: in silico definition and in vivo characterization by proteomics of normal and tumor extracellular matrices.Mol Cell Proteomics. 2012; 11 (M111): 014647Abstract Full Text Full Text PDF PubMed Scopus (0) Google Scholar,45Todorović V. Desai B.V. Eigenheer R.A. et al.Detection of differentially expressed basal cell proteins by mass spectrometry.Mol Cell Proteomics. 2010; 9: 351-361Abstract Full Text Full Text PDF PubMed Scopus (0) Google Scholar,46Didangelos A. Yin X. Mandal K. et al.Proteomics characterization of extracellular space components in the human aorta.Mol Cell Proteomics. 2010; 9: 2048-2062Abstract Full Text Full Text PDF PubMed Scopus (209) Google Scholar separate cellular proteins from matrix proteins according to their detergent solubility. This technique increases the resolution of matrix proteins in proteomics experiments and has led to the definition of tissue matrisomes, including liver,47Baiocchini A. Montaldo C. 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Humphries J.D. et al.Global analysis reveals the complexity of the human glomerular extracellular matrix.J Am Soc Nephrol. 2014; 25: 939-951Crossref PubMed Scopus (115) Google Scholar and various tumors.51Socovich A.M. Naba A. The cancer matrisome: from comprehensive characterization to biomarker discovery.Semin Cell Dev Biol. 2019; 89: 157-166Crossref PubMed Scopus (68) Google Scholar Furthermore, spatial proteomics, using laser capture from tissue sections, such as glomerular isolation, can also aid in specific proteome definitions. The goal of holistic proteomic studies should not only be to profile composition, but to go further and characterize localization. Usually, this is achieved via complementary immunolocalization approaches once the matrisome is defined. Ideally, these approaches would match the data output of proteomics; however, the most commonly applied is immunofluorescence imaging, which is comparatively low throughput. Other mass spectrometry techniques, such as mass spectrometry imaging, may present novel avenues for global analysis of matrix proteins. These experiments aim to couple identification, quantification, and localization of proteins within a single experiment. These techniques include matrix-assisted laser desorption/ionization, time-of-flight-secondary ion mass spectrometry, and electrospray-based desorption. Although these techniques are well established, in particular for metabolite detection, there is a trade-off in proteomics; using mass spectrometry imaging, the number of identified proteins is limited to the most abundant 5% of proteins present in the tissue.52Spraggins J.M. Rizzo D.G. Moore J.L. et al.MALDI FTICR IMS of intact proteins: using mass accuracy to link protein images with proteomics data.J Am Soc Mass Spectrom. 2015; 26: 974-985Crossref PubMed Scopus (74) Google Scholar, 53van de Ven S.M.W.Y. Bemis K.D. 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Posted online April 14, 2021. https://doi.org/10.1101/2021.04.14.439828.Google Scholar Thus far, these techniques have yet to be applied to kidney tissue, or specifically for the identification of matrix. However, there appears to be no slowing of progression in mass spectrometry technologies, with increases in sensitivity revealing more complexity and facilitating downscaling of required starting material. Together, these advances will facilitate a greater understanding of kidney matrix composition in health and disease. The complexity of the glomerular matrisome has been interrogated by several research groups using proteomics.50Lennon R. Byron A. Humphries J.D. et al.Global analysis reveals the complexity of the human glomerular extracellular matrix.J Am Soc Nephrol. 2014; 25: 939-951Crossref PubMed Scopus (115) Google Scholar,59Randles M.J. Woolf A.S. Huang J.L. et al.Genetic background is a key determinant of glomerular extracellular matrix composition and organization.J Am Soc Nephrol. 2015; 26: 3021-3034Crossref PubMed Scopus (32) Google Scholar,60Hobeika L. Barati M.T. Caster D.J. et al.Characterization of glomerular extracellular matrix by proteomic analysis of laser-captured microdissected glomeruli.Kidney Int. 2017; 91: 501-511Abstract Full Text Full Text PDF PubMed Google Scholar Surprisingly, the complexity of this niche was far beyond the limited number of previously known components, with 144 proteins catalogued from native human kidneys unsuitable for transplantation in 2014.50Lennon R. Byron A. Humphries J.D. et al.Global analysis reveals the complexity of the human glomerular extracellular matrix.J Am Soc Nephrol. 2014; 25: 939-951Crossref PubMed Scopus (115) Google Scholar Similar experiments were performed in mouse models, revealing significant overlap of human and mouse glomerular matrisomes.59Randles M.J. Woolf A.S. Huang J.L. et al.Genetic background is a key determinant of glomerular extracellular matrix composition and organization.J Am Soc Nephrol. 2015; 26: 3021-3034Crossref PubMed Scopus (32) Google Scholar This identified cross-species similarity in glomerular matrix composition allowed for disease-modeling studies in mice, which circumvents the limited availability of human tissue. In contrast to studying mouse tissue, human patient biopsies are small in size and formalin fixed and paraffin embedded. Often, this means that biopsies contain only few glomeruli, limiting starting material and restricting protein identification to more abundant proteins. Aiming to overcome these hurdles, in 2012, laser-microdissected glomeruli from formalin-fixed, paraffin-embedded tissue were investigated for protein signatures in diabetic nephropathy.61Nakatani S. Wei M. Ishimura E. et al.Proteome analysis of laser microdissected glomeruli from formalin-fixed paraffin-embedded kidneys of autopsies of diabetic patients: nephronectin is associated with the development of diabetic glomerulosclerosis.Nephrol Dial Transplant. 2012; 27: 1889-1897Crossref PubMed Google Scholar This study identified 100 proteins with altered abundance in diabetic nephropathy, including 28 matrix components. Although this study pioneered the approach to formalin-fixed, paraffin-embedded glomerular proteomics, the number of identified proteins overall was limited. Potentially because of the limited starting material, whole tissue was used, rather than enriching specifically for matrix proteins, which might explain the limited number of matrix proteins identified. A study from 2017 improved sample preparation from formalin-fixed, paraffin-embedded human tissue and applied an adapted matrix enrichment approach. Concordantly, this study confirmed the identification of a complex matrisome niche of 147 proteins from glomeruli, from just 100 sections (10 μm thick).60Hobeika L. Barati M.T. Caster D.J. et al.Characterization of glomerular extracellular matrix by proteomic analysis of laser-captured microdissected glomeruli.Kidney Int. 2017; 91: 501-511Abstract Full Text Full Text PDF PubMed Google Scholar Moreover, this new approach was used to investigate the diseased glomerular matrisome in focal segmental glomerular sclerosis (FSGS). This study identified a glomerular matrisome of 166 components, of which 58 proteins differed in abundance in FSGS compared with control.62Merchant M.L. Barati M.T. Caster D.J. et al.Proteomic analysis identifies distinct glomerular extracellular matrix in collapsing focal segmental glomerulosclerosis.J Am Soc Nephrol. 2020; 31: 1883-1904Crossref PubMed Scopus (16) Google Scholar In addition to FSGS, the glomerular matrisome was investigated using laser-captured glomeruli and matrix enrichment in IgA nephropathy (IgAN).63Paunas F.T.I. Finne K. Leh S. et al.Characterization of glomerular extracellular matrix in IgA nephropathy by proteomic analysis of laser-captured microdissected glomeruli.BMC Nephrol. 2019; 20: 410Crossref PubMed Scopus (10) Google Scholar This study identified 179 glomerular matrisome proteins, with 56 having altered abundance in IgAN. More recent research uncovered the aging human glomerular matrisome, identifying 171 components, with 29 proteins showing association with age.4Randles M. Lausecker F. Kong Q. et al.Identification of an altered matrix signature in kidney aging and disease.J Am Soc Nephrol. 2021; 32: 1713-1732Crossref Scopus (9) Google Scholar By combining these 6 distinct proteomic studies, the glomerular "master matrisome" comprises 288 proteins with a consensus 51 proteins detected across all data sets that included matrix enrichment (Figure 2). The variation in protein identification across different data sets is likely due to low abundance of proteins with few tryptic peptides and peptides that are refractory to detection. Although human tissue studies are clearly vital, mouse models allow